Variant report

Variant	rs12568144
Chromosome Location	chr1:45965307-45965308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:45965281-45965854	H1-hESC	embryonic stem cell:	n/a	n/a
2	RELA	chr1:45965145-45966187	GM15510	blood:	n/a	n/a
3	ZNF143	chr1:45965225-45966236	K562	blood:	n/a	n/a
4	REST	chr1:45965144-45966351	H1-neurons	neurons:	n/a	n/a
5	GTF2F1	chr1:45965158-45966177	K562	blood:	n/a	n/a
6	SP1	chr1:45965222-45966316	HCT-116	colon:	n/a	n/a
7	HCFC1	chr1:45964803-45966980	Hela-S3	cervix:	n/a	n/a
8	SPI1	chr1:45965186-45966183	HL-60	blood:	n/a	n/a
9	MTA3	chr1:45965191-45966319	GM12878	blood:	n/a	n/a
10	ZBTB7A	chr1:45964963-45965413	K562	blood:	n/a	n/a
11	MXI1	chr1:45964964-45967174	SK-N-SH	brain:	n/a	n/a
12	KAP1	chr1:45965162-45966254	HEK293	kidney:	n/a	n/a
13	SIN3A	chr1:45965295-45966191	GM12878	blood:	n/a	n/a
14	SMARCC2	chr1:45964799-45966165	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr1:45965160-45965310	GM12873	blood:	n/a	n/a
16	SMC3	chr1:45965142-45966111	K562	blood:	n/a	n/a
17	POLR2A	chr1:45964582-45967225	HepG2	liver:	n/a	n/a
18	EP300	chr1:45965277-45966190	GM12878	blood:	n/a	n/a
19	HCFC1	chr1:45965212-45966257	K562	blood:	n/a	n/a
20	CTCF	chr1:45965200-45965350	NB4	blood:	n/a	n/a
21	MTA3	chr1:45964977-45966341	GM12878	blood:	n/a	n/a
22	ZNF143	chr1:45965233-45966226	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:45965218-45966367	SK-N-MC	brain:	n/a	n/a
24	WRNIP1	chr1:45964987-45966163	GM12878	blood:	n/a	n/a
25	RUNX3	chr1:45965098-45966212	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:45965129-45966274	Raji	blood:	n/a	n/a
27	IRF4	chr1:45965281-45966185	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:45965055-45966317	K562	blood:	n/a	n/a
29	PML	chr1:45965215-45966281	K562	blood:	n/a	n/a
30	MXI1	chr1:45965256-45966245	HepG2	liver:	n/a	n/a
31	TEAD4	chr1:45965248-45966332	K562	blood:	n/a	n/a
32	MAX	chr1:45965249-45966300	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:45965163-45966336	PFSK-1	brain:	n/a	n/a
34	RCOR1	chr1:45965251-45966248	GM12878	blood:	n/a	n/a
35	E2F4	chr1:45965043-45966263	K562	blood:	n/a	n/a
36	MYC	chr1:45965252-45966279	K562	blood:	n/a	n/a
37	TCF7L2	chr1:45965174-45966219	Hela-S3	cervix:	n/a	n/a
38	MAX	chr1:45965284-45966320	H1-hESC	embryonic stem cell:	n/a	n/a
39	CREB1	chr1:45965269-45966354	K562	blood:	n/a	n/a
40	STAT5A	chr1:45965175-45966332	GM12878	blood:	n/a	n/a
41	CREB1	chr1:45965284-45966338	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:45964960-45966439	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTBP2	chr1:45965154-45966279	H1-hESC	embryonic stem cell:	n/a	n/a
44	SMARCC1	chr1:45964918-45966156	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr1:45965254-45966349	K562	blood:	n/a	n/a
46	SIN3AK20	chr1:45965290-45966280	K562	blood:	n/a	n/a
47	CTCF	chr1:45965220-45965370	HEEpiC	esophagus:	n/a	n/a
48	SIN3AK20	chr1:45965243-45966161	PANC-1	pancreas:	n/a	n/a
49	MAX	chr1:45965205-45966342	HepG2	liver:	n/a	n/a
50	MAX	chr1:45965189-45966357	HCT-116	colon:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
2	chr1:45185969..45188598-chr1:45964540..45967567,4	K562	blood:
3	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
4	chr1:45806085..45807923-chr1:45963911..45966246,2	MCF-7	breast:
5	chr1:45768003..45772070-chr1:45964648..45967315,5	K562	blood:
6	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
7	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
8	chr1:45265558..45267516-chr1:45964222..45967034,2	K562	blood:
9	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
10	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:
11	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
12	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:
13	chr1:45804471..45806506-chr1:45965051..45967533,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TESK2-1	chr1:45965204-45965751	NR_033298
2	lnc-TESK2-1	chr1:45965204-45965751	NR_033297
3	lnc-TESK2-1	chr1:45965204-45965751	NR_033296

No data

Variant related genes	Relation type
CCDC163P	TF binding region
MMACHC	TF binding region
ENSG00000132773	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10789465	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10890331	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11211109	0.90[ASN][1000 genomes]
rs11211122	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211130	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211135	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211136	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11580609	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11582118	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12119202	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12133294	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12139364	0.87[ASN][1000 genomes]
rs12729715	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12738318	0.92[ASN][1000 genomes]
rs12743512	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1765709	0.83[ASN][1000 genomes]
rs2036021	0.86[ASN][1000 genomes]
rs2275276	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2356413	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2356551	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2356553	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2492841	0.87[ASN][1000 genomes]
rs2934856	0.81[EUR][1000 genomes]
rs2934859	0.81[EUR][1000 genomes]
rs2991970	0.84[EUR][1000 genomes]
rs2991972	0.81[EUR][1000 genomes]
rs2991973	0.80[EUR][1000 genomes]
rs2991974	0.80[EUR][1000 genomes]
rs2993262	0.81[EUR][1000 genomes]
rs35092140	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4660859	0.86[ASN][1000 genomes]
rs4660861	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4660869	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4660876	0.81[EUR][1000 genomes]
rs512026	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs518365	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs523526	0.81[EUR][1000 genomes]
rs60608374	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs622798	0.81[EUR][1000 genomes]
rs644915	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6661321	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs667626	0.81[EUR][1000 genomes]
rs71500084	0.85[ASN][1000 genomes]
rs7526571	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7526665	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs781058	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7903	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9147	0.81[EUR][1000 genomes]
rs937291	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429079	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs945180	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998199	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12568144	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs12568144	CCDC163P	cis	Artery Aorta	GTEx
rs12568144	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs12568144	CCDC163P	cis	Muscle Skeletal	GTEx
rs12568144	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12568144	CCDC163P	cis	Stomach	GTEx
rs12568144	CCDC163P	cis	Esophagus Mucosa	GTEx
rs12568144	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12568144	CCDC163P	cis	Thyroid	GTEx
rs12568144	CCDC163P	cis	Nerve Tibial	GTEx
rs12568144	CCDC163P	cis	lung	GTEx
rs12568144	GPBP1L1	cis	Whole Blood	GTEx
rs12568144	CCDC163P	cis	Heart Left Ventricle	GTEx
rs12568144	CCDC163P	cis	Artery Tibial	GTEx
rs12568144	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12568144	CCDC163P	cis	Whole Blood	GTEx
rs12568144	IPP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
2	chr1:45964400-45965400	Flanking Active TSS	Brain Anterior Caudate	brain
3	chr1:45964400-45965400	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr1:45964400-45965400	Flanking Active TSS	Dnd41	blood
5	chr1:45964400-45966600	Active TSS	A549	lung
6	chr1:45964400-45966800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:45964600-45965400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:45964600-45965400	Flanking Active TSS	GM12878-XiMat	blood
9	chr1:45964600-45965400	Flanking Active TSS	NHEK	skin
10	chr1:45964600-45965600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr1:45964600-45965600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:45964600-45965600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr1:45964600-45965600	Flanking Active TSS	Hela-S3	cervix
14	chr1:45964600-45966600	Active TSS	Rectal Smooth Muscle	rectum
15	chr1:45964800-45965400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:45964800-45965400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr1:45964800-45965400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:45964800-45965400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:45964800-45965400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:45964800-45965400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr1:45964800-45965400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:45964800-45965400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:45964800-45965400	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr1:45964800-45965400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:45964800-45965400	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr1:45964800-45965400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:45964800-45965400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr1:45964800-45965400	Flanking Active TSS	Right Ventricle	heart
29	chr1:45964800-45965400	Flanking Active TSS	Thymus	Thymus
30	chr1:45964800-45965400	Flanking Active TSS	HMEC	breast
31	chr1:45964800-45965600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr1:45964800-45965600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr1:45964800-45965600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr1:45964800-45965600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:45964800-45965600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr1:45964800-45965600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr1:45964800-45965600	Flanking Active TSS	K562	blood
38	chr1:45964800-45965600	Flanking Active TSS	Osteobl	bone
39	chr1:45964800-45966200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:45964800-45966600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr1:45964800-45966600	Active TSS	Ovary	ovary
42	chr1:45964800-45967200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:45964800-45967400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:45965000-45965400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:45965000-45965400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:45965000-45965400	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr1:45965000-45965400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:45965000-45965400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:45965000-45965400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:45965000-45965400	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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